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PeterPetriknyalldawson
PeterPetrik
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nyalldawson
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update MDAL to 0.0.7 (3di support, projections support, bugfixes)
1 parent d17912c commit 97c9580

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+1147
-20
lines changed

‎external/mdal/api/mdal.h

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@@ -83,6 +83,11 @@ MDAL_EXPORT MeshH MDAL_LoadMesh( const char *meshFile );
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//! Closes mesh, frees the memory
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MDAL_EXPORT void MDAL_CloseMesh( MeshH mesh );
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/**
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* Returns mesh projection
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* not thread-safe and valid only till next call
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*/
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MDAL_EXPORT const char *MDAL_M_projection( MeshH mesh );
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//! Returns vertex count for the mesh
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MDAL_EXPORT int MDAL_M_vertexCount( MeshH mesh );
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//! Returns vertex X coord for the mesh

‎external/mdal/cmake/FindNetCDF.cmake

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# - Find NetCDF
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# Find the native NetCDF includes and library
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# Copyright (c) 2018, Peter Petrik <zilolv at gmail dot com>
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#
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# This module returns these variables for the rest of the project to use.
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#
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# NETCDF_FOUND - True if NetCDF found including required interfaces (see below)
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# NETCDF_LIBRARY - All netcdf related libraries
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# NETCDF_INCLUDE_DIR - All directories to include
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IF (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
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# Already in cache, be silent
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SET (NETCDF_FIND_QUIETLY TRUE)
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ENDIF ()
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FIND_PACKAGE(PkgConfig)
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PKG_CHECK_MODULES(PC_NETCDF QUIET netcdf)
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SET(NETCDF_DEFINITIONS ${PC_NETCDF_CFLAGS_OTHER})
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FIND_PATH (NETCDF_INCLUDE_DIR netcdf.h
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HINTS ${PC_NETCDF_INCLUDEDIR} ${PC_NETCDF_INCLUDE_DIRS} ${NETCDF_PREFIX}/include
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PATH_SUFFIXES libnetcdf )
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FIND_LIBRARY (NETCDF_LIBRARY
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NAMES netcdf libnetcdf
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HINTS HINTS ${PC_NETCDF_LIBDIR} ${PC_NETCDF_LIBRARY_DIRS} ${NETCDF_PREFIX}/lib)
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INCLUDE (FindPackageHandleStandardArgs)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS (NetCDF
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DEFAULT_MSG NETCDF_LIBRARY NETCDF_INCLUDE_DIR)
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‎external/mdal/cmake_templates/mdal_config.hpp.in

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@@ -7,6 +7,8 @@
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#cmakedefine HAVE_GDAL
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#cmakedefine HAVE_NETCDF
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#endif // MDAL_CONFIG_HPP
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‎external/mdal/frmts/mdal_3di.cpp

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/*
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MDAL - Mesh Data Abstraction Library (MIT License)
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Copyright (C) 2018 Peter Petrik (zilolv at gmail dot com)
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*/
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#include "mdal_3di.hpp"
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MDAL::Loader3Di::Loader3Di( const std::string &fileName )
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: LoaderCF( fileName )
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{
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}
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MDAL::CFDimensions MDAL::Loader3Di::populateDimensions()
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{
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CFDimensions dims;
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size_t count;
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int ncid;
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// 2D Mesh
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mNcFile.getDimension( "nMesh2D_nodes", &count, &ncid );
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dims.setDimension( CFDimensions::Face2D, count, ncid );
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mNcFile.getDimension( "nCorner_Nodes", &count, &ncid );
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dims.setDimension( CFDimensions::MaxVerticesInFace, count, ncid );
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// Vertices count is populated later in populateFacesAndVertices
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// it is not known from the array dimensions
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// Time
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mNcFile.getDimension( "time", &count, &ncid );
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dims.setDimension( CFDimensions::Time, count, ncid );
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return dims;
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}
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void MDAL::Loader3Di::populateFacesAndVertices( MDAL::Mesh *mesh )
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{
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assert( mesh );
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size_t faceCount = mDimensions.size( CFDimensions::Face2D );
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mesh->faces.resize( faceCount );
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size_t verticesInFace = mDimensions.size( CFDimensions::MaxVerticesInFace );
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size_t arrsize = faceCount * verticesInFace;
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std::map<std::string, size_t> xyToVertex2DId;
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// X coordinate
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int ncidX = mNcFile.getVarId( "Mesh2DContour_x" );
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double fillX = mNcFile.getFillValue( ncidX );
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std::vector<double> faceVerticesX( arrsize );
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if ( nc_get_var_double( mNcFile.handle(), ncidX, faceVerticesX.data() ) ) throw MDAL_Status::Err_UnknownFormat;
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// Y coordinate
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int ncidY = mNcFile.getVarId( "Mesh2DContour_y" );
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double fillY = mNcFile.getFillValue( ncidY );
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std::vector<double> faceVerticesY( arrsize );
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if ( nc_get_var_double( mNcFile.handle(), ncidY, faceVerticesY.data() ) ) throw MDAL_Status::Err_UnknownFormat;
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// now populate create faces and backtrack which vertices
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// are used in multiple faces
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for ( size_t faceId = 0; faceId < faceCount; ++faceId )
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{
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Face face;
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for ( size_t faceVertexId = 0; faceVertexId < verticesInFace; ++faceVertexId )
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{
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size_t arrId = faceId * verticesInFace + faceVertexId;
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Vertex vertex;
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vertex.x = faceVerticesX[arrId];
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vertex.y = faceVerticesY[arrId];
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vertex.z = 0;
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if ( MDAL::equals( vertex.x, fillX ) || MDAL::equals( vertex.y, fillY ) )
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break;
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size_t vertexId;
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std::string key = std::to_string( vertex.x ) + "," + std::to_string( vertex.y );
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const auto it = xyToVertex2DId.find( key );
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if ( it == xyToVertex2DId.end() )
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{
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// new vertex
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vertexId = mesh->vertices.size();
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xyToVertex2DId[key] = vertexId;
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mesh->vertices.push_back( vertex );
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}
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else
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{
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// existing vertex
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vertexId = it->second;
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}
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face.push_back( vertexId );
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}
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mesh->faces[faceId] = face;
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}
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// Only now we have number of vertices, since we identified vertices that
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// are used in multiple faces
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mDimensions.setDimension( CFDimensions::Vertex2D, mesh->vertices.size() );
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}
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void MDAL::Loader3Di::addBedElevation( MDAL::Mesh *mesh )
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{
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assert( mesh );
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if ( mesh->faces.empty() )
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return;
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size_t faceCount = mesh->faces.size();
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// read Z coordinate of 3di computation nodes centers
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int ncidZ = mNcFile.getVarId( "Mesh2DFace_zcc" );
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double fillZ = mNcFile.getFillValue( ncidZ );
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std::vector<double> coordZ( faceCount );
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if ( nc_get_var_double( mNcFile.handle(), ncidZ, coordZ.data() ) )
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return; //error reading the array
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std::shared_ptr<DatasetGroup> group = std::make_shared< DatasetGroup >();
121+
group->isOnVertices = false;
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group->isScalar = true;
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group->setName( "Bed Elevation" );
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group->uri = mesh->uri;
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std::shared_ptr<MDAL::Dataset> dataset = std::make_shared< Dataset >();
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dataset->time = 0.0;
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dataset->values.resize( faceCount );
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dataset->active.resize( faceCount );
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dataset->parent = group.get();
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for ( size_t i = 0; i < faceCount; ++i )
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{
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dataset->values[i].x = MDAL::safeValue( coordZ[i], fillZ );
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}
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group->datasets.push_back( dataset );
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mesh->datasetGroups.push_back( group );
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}
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std::string MDAL::Loader3Di::getCoordinateSystemVariableName()
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{
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return "projected_coordinate_system";
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}
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std::set<std::string> MDAL::Loader3Di::ignoreNetCDFVariables()
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{
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std::set<std::string> ignore_variables;
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ignore_variables.insert( "projected_coordinate_system" );
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ignore_variables.insert( "time" );
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std::vector<std::string> meshes;
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meshes.push_back( "Mesh1D" );
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meshes.push_back( "Mesh2D" );
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for ( const std::string &mesh : meshes )
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{
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ignore_variables.insert( mesh );
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ignore_variables.insert( mesh + "Node_id" );
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ignore_variables.insert( mesh + "Node_type" );
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ignore_variables.insert( mesh + "Face_xcc" );
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ignore_variables.insert( mesh + "Face_ycc" );
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ignore_variables.insert( mesh + "Face_zcc" );
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ignore_variables.insert( mesh + "Contour_x" );
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ignore_variables.insert( mesh + "Contour_y" );
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ignore_variables.insert( mesh + "Face_sumax" );
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ignore_variables.insert( mesh + "Line_id" );
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ignore_variables.insert( mesh + "Line_xcc" );
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ignore_variables.insert( mesh + "Line_ycc" );
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ignore_variables.insert( mesh + "Line_zcc" );
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ignore_variables.insert( mesh + "Line_type" );
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}
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return ignore_variables;
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}
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std::string MDAL::Loader3Di::nameSuffix( MDAL::CFDimensions::Type type )
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{
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MDAL_UNUSED( type );
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return "";
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}
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void MDAL::Loader3Di::parseNetCDFVariableMetadata( int varid, const std::string &variableName, std::string &name, bool *is_vector, bool *is_x )
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{
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*is_vector = false;
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*is_x = true;
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std::string long_name = mNcFile.getAttrStr( "long_name", varid );
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if ( long_name.empty() )
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{
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std::string standard_name = mNcFile.getAttrStr( "standard_name", varid );
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if ( standard_name.empty() )
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{
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name = variableName;
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}
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else
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{
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if ( MDAL::contains( standard_name, "_x_" ) )
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{
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*is_vector = true;
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name = MDAL::replace( standard_name, "_x_", "" );
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}
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else if ( MDAL::contains( standard_name, "_y_" ) )
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{
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*is_vector = true;
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*is_x = false;
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name = MDAL::replace( standard_name, "_y_", "" );
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}
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else
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{
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name = standard_name;
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}
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}
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}
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else
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{
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if ( MDAL::contains( long_name, " in x direction" ) )
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{
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*is_vector = true;
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name = MDAL::replace( long_name, " in x direction", "" );
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}
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else if ( MDAL::contains( long_name, " in y direction" ) )
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{
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*is_vector = true;
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*is_x = false;
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name = MDAL::replace( long_name, " in y direction", "" );
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}
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else
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{
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name = long_name;
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}
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}
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}

‎external/mdal/frmts/mdal_3di.hpp

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@@ -0,0 +1,62 @@
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/*
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MDAL - Mesh Data Abstraction Library (MIT License)
3+
Copyright (C) 2018 Peter Petrik (zilolv at gmail dot com)
4+
*/
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#ifndef MDAL_3DI_HPP
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#define MDAL_3DI_HPP
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#include <map>
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#include <string>
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#include <stddef.h>
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#include "mdal_cf.hpp"
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namespace MDAL
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{
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/**
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* Loader of 3Di file format.
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*
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* The result 3Di NetCDF file is based on CF-conventions with some additions.
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* It is unstructured grid with data stored in NetCDF/HDF5 file format.
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* A division is made between a 1D and 2D which can be distinguished through
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* the prefixes “MESH2D” and “MESH1D”. For both meshes the information is present
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* in coordinate, id, and type variables.
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*
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* A version of the data scheme is not present yet.
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*
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* The 2D Mesh consists of calculation Nodes that represents centers of Faces.
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* There is no concept of Vertices in the file. The vertices that forms a face
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* are specified by X,Y coordinates in the "Face Contours" arrays. The "lines"
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* represent the face's edges and are again specified by X,Y coordinate of the
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* line center. Data is specified on calculation nodes (i.e. dataset defined on faces)
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* and on lines (i.e. dataset defined on edges - not implemented yet)
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*
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* The 1D Mesh is present too, but not parsed yet.
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*/
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class Loader3Di: public LoaderCF
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{
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public:
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Loader3Di( const std::string &fileName );
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~Loader3Di() override = default;
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private:
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CFDimensions populateDimensions() override;
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void populateFacesAndVertices( MDAL::Mesh *mesh ) override;
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void addBedElevation( MDAL::Mesh *mesh ) override;
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std::string getCoordinateSystemVariableName() override;
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std::set<std::string> ignoreNetCDFVariables() override;
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std::string nameSuffix( CFDimensions::Type type ) override;
51+
void parseNetCDFVariableMetadata( int varid, const std::string &variableName,
52+
std::string &name, bool *is_vector, bool *is_x ) override;
53+
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//! Returns number of vertices
55+
size_t parse2DMesh();
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void addBedElevationDatasetOnFaces();
58+
};
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} // namespace MDAL
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#endif // MDAL_3DI_HPP

‎external/mdal/frmts/mdal_ascii_dat.cpp

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Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ void MDAL::LoaderAsciiDat::load( MDAL::Mesh *mesh, MDAL_Status *status )
6969
oldFormat = true;
7070
isVector = ( line == "VECTOR" );
7171

72-
group.reset( new DatasetGroup() );
72+
group = std::make_shared< DatasetGroup >();
7373
group->uri = mDatFile;
7474
group->setName( name );
7575
group->isScalar = !isVector;
@@ -118,7 +118,7 @@ void MDAL::LoaderAsciiDat::load( MDAL::Mesh *mesh, MDAL_Status *status )
118118
}
119119
isVector = cardType == "BEGVEC";
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121-
group.reset( new DatasetGroup() );
121+
group = std::make_shared< DatasetGroup >();
122122
group->uri = mDatFile;
123123
group->setName( name );
124124
group->isScalar = !isVector;
@@ -197,7 +197,7 @@ void MDAL::LoaderAsciiDat::readVertexTimestep(
197197
size_t vertexCount = mesh->vertices.size();
198198
size_t faceCount = mesh->faces.size();
199199

200-
std::shared_ptr<MDAL::Dataset> dataset( new MDAL::Dataset );
200+
std::shared_ptr<MDAL::Dataset> dataset = std::make_shared< MDAL::Dataset >();
201201
dataset->time = t / 3600.; // TODO read TIMEUNITS
202202
dataset->values.resize( vertexCount );
203203
dataset->active.resize( faceCount );
@@ -267,7 +267,7 @@ void MDAL::LoaderAsciiDat::readFaceTimestep(
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268268
size_t faceCount = mesh->faces.size();
269269

270-
std::shared_ptr<MDAL::Dataset> dataset( new MDAL::Dataset );
270+
std::shared_ptr<MDAL::Dataset> dataset = std::make_shared< MDAL::Dataset >();
271271
dataset->time = t / 3600.;
272272
dataset->values.resize( faceCount );
273273
dataset->parent = group.get();

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